An End Once and for All
by LuvMira
Summary: MAJOR IN-DEPTH SPOILER ALERT: This fanfiction takes place after ME3. What if the ending we were told was a lie, a happy ending that left Shepard a legend for the young to hear about in future? What if what really happened was not so "legendary" as we were told? The Reapers are far from finished with the universe and Shepard learns exactly what it means to be human. Faults and all.


**WARNINGS:** There will be adult content in this fanfiction, seeing as the game is pretty mature itself. Also, this fanfiction occurs after the end of Mass Effect 3 so it jumps right into spoiler area. If you do not want to be spoiled, do not read ahead.

**DISCLAIMER:** I do not own anything of the Mass Efffect universe. Airyn Shepard is my paragon I had nothing to do with the creation of the Indoctrination Theory either. I just thought it'd be an interesting take for a fanfiction.

Also,** fair warning**. I will be participating in NaNoWriMo, so November will be full pretty inactive. I will still try to update, though it may take some time. I thank you for your patience in advance. Please enjoy the story. ^^

_"Memory reconstruction at eighty-three percent..."_

"We did it."

"Yes, we did. It's quite a view."

_"Memory reconstruction at eighty-seven percent..."_

"You're slow, Shepard!"

"I'm only slow because I'm not running!"

_"Memory reconstruction at ninety-five percent..."_

"Had to be me. Someone else might have gotten it wrong."

"Good luck out there, Lola."

"Guess we're old soldiers, hey Shepard?"

"Good luck, Shepard. If you live through it, drinks are on me."

"I won't let you down, Shepard. Go kick some ass."

"Go out there and give them hell. You were born to do this."

"The Illusive Man ordered my creation years ago. Jeff was the one who allowed me to think for myself. But only now do I feel alive. That is your influence.

_"Memory reconstruction at one hundred percent._

_Welcome back, Shepard."_

"It's about time you started to wake up, Shepard. I thought I couldn't work another miracle for a second there."

A voice permeated the darkness that surrounded the once dead Commander Shepard. Her body felt well rested, like she had just awoken from a well deserved rest. The only problem was that everything seemed so hypersensitive at this point. Her ears picked up on sounds she had never noticed before and when she tried to open her eyes, the light seemed to nearly blind her.

Where was she? And what had happened?

"Shepard? Can you hear me?"

"More than I would like to," the Commander said, her body rising up as her hand instinctively went to rest on her now throbbing head.

What she felt was not something from memory. She felt metal, a large amount of it.

"Please lie back down, Commander. You're not healthy enough to start running around. We had a lot less to deal with this time." The light took a bit to adjust to, but Shepard could still make out the moving form of Miranda Lawson rushing towards her. Her old friend was once again hovering over her in what seemed like a lab. This time, the woman seemed more concerned about the commander rather than a project she had been conducting.

"Ugh..." The hand of the woman pressed down on the commander's shoulder, showing that her muscles still seemed pretty hyper-sensitive. She must not be done with repairs.

Or whatever happened.

"What happened? Did we fight the Reapers off?"

Her friend merely chuckled as she grabbed a syringe, the liquid a strange color and it seemed to change shade as pressure was placed on it. "Shepard, when will you ever learn to take it easy?" But as she injected the gelatinous substance into the commander's body, Shepard noticed the sadness in the other woman's voice and eyes.

Did the Reapers still exist? Were they still hell-bent on destroying life in the universe?

"Miranda-"

Before anymore questions could be asked, the sounds of a door opening and a familiar voice interrupted the two women.

"I see that you still can't be put down, Shepard."

Turning to look in the direction of the voice, Shepard saw one of her most loyal -and sometimes conflicted- comrades. Garrus Vakarian.

A smile formed on her face as the Turian walked towards her, a notable limp in his step. He had been with her on her run towards the beam to reach the Citadel. He'd been badly injured then and it was obvious that it would have some lasting effects.

"There's no Shepard without Vakarian. Glad to see you're still kicking." It was odd looking at Garrus while lying on an operating table. But she was far too happy to care.

"Likewise." The Turian smiled slightly, the scar on his face stretching slightly. This guy had been put through Hell and back; yet, he remained at the commander's side. She was very grateful for such a friend.

Miranda then injected something else in her legs, her nerves now feeling the large needle insert itself in her skin. She winced slightly, though no one would have noticed from the sudden shake of the vessel.

"What was that?"

Shepard instinctively shot up and looked around her, trying to find a weapon but this time Garrus was the one to hold her back.

"Don't worry. We're almost out of their firing range. Joker and EDI have things handled." The Turian tried to smile, much like Miranda had earlier, with the exact same sadness lining his voice.

What the hell was going on?

"No. I want answers. Why do you both act like this war isn't over?" No more, Ms. Nice Shepard. She needed answers and she couldn't just sit by and act like a patient when things seemed dire. She was Commander Shepard of the Alliance, Spectre for the Council, and savior of the galaxy.

The two stopped what they were doing, their eyes averted from their commanding officer. Great. Things were going to hell while she was gone.

"Commander... Do you not remember what happened after you entered the beam?" Miranda had stepped back, her arms crossed and her eyes quizzically scanning the other woman.

Trying to think fast, the woman looked away from the other and thought over what had occurred.

The Illusive Man had been there and tried to indoctrinate her. She shot Anderson while trying to fight it... She passed out as the Crucible was placed and...

The Child had told her of its purpose, of its desire to end chaos and allowed her to choose the outcome.

What had she chosen? What happened after that?

"I remember the Citadel was no longer the same. It was littered with human bodies. Anderson was there and so was the Illusive Man. They tried to indoctrinate me and-"

"'They'?" Shepard looked to Garrus, the confusion very apparent in his eyes. Did she say they? But why?

"I mean 'he'. The Illusive Man tried to indoctrinate me. He made me shoot the Captain right before..." Things grew cloudy at that point. What had happened to the Illusive Man?

"He shot himself. I tried to reason with him, to let him know he was the one being indoctrinated. I think I got through to him. And after that, the Crucible was set in place once I opened the arms of the Citadel. And..." She thought harder, the memories seeming to fade more and more and time passed. "Nothing happened until I was raised to some foreign location. An A.I. in the shape of child was there."

"A child?" Garrus looked her over again, seeming to know something that she did not. But Miranda cleared her throat, getting the commander's attention again. Apparently, she needed the story to continue. But why?

"Yeah, it mentioned that it was created in the beginning to uphold order. It controlled the Reapers and it allowed me to make a choice. I could control them, seeing as I was not under their influence like the Illusive Man. I could destroy it which would end all synthetic life, not just the Reapers. Or I could choose synthesis."

"What's synthesis?" This time, Miranda was the one to chime in.

"It said that I could sacrifice myself in order to meld synthetic and organic life together." Shepard placed a hand on her forehead, now feeling the overwhelming headache she had brought on herself. "Only by destroying all synthetic life would I supposedly walk away alive, though it was still a gamble. I'm part synthetic already."

The commander tried to laugh that part off, now feeling a little odd in the silence. But the other two did not laugh with her. Instead, they seemed to be thinking very hard.

"What did you choose," Miranda finally asked, her voice oddly hushed.

Shepard tried to think over it some more, but couldn't find an answer. What had she chosen?

And if she had, wouldn't the choice be obvious in the world now?

"I... I can't remember," she answered truthfully, her memories now fading to white and restarting when she awoke on the table. "Everything goes blank after that."

Miranda and Garrus exchanged a look then, one of concern and almost understanding.

Shepard frowned as she looked between them. "What? What happened?"

The woman above her shook her head with pained eyes. And the words that left her lips then terrified the commander.

"I'm afraid you were... indoctrinated, Commander."

**AUTHOR'S NOTE (A/N): **That's the prologue. ^^ I hope you enjoyed and I will try to get this updated as soon as possible. If you're the encouraging (or critcal type) please leave a review and I will think over your comment as I write the next chapter. Thank you!


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